President Barack Obama on Tuesday pardoned a retired U.S. Marine Corps general who pleaded guilty in October to making false statements to the FBI during an investigation into leaks of classified information.

James Cartwright, who last served as vice chairman of the Joint Chiefs of Staff, was questioned by the Federal Bureau of Investigation in 2012.

He was asked about a book written by New York Times reporter David Sanger, which exposed a malicious computer software program known as 'Stuxnet' designed to disrupt Iran's nuclear program.

James Cartwright pleaded guilty to making false statements during a federal probe after classified information was leaked to New York Times journalist David Sanger

Cartwright, who was appointed the second-highest military officer by George W. Bush and dubbed Barack Obama's favorite general by Robert Woodward, was investigated in 2013 after Sanger named him as a key player in the operation code-named Olympic Games

Sanger (pictured) wrote extensively about Stuxnet in a book and multiple reports in the Times

Cartwright, 67, had denied slipping out classified details to two New York Times reporters in a 2012 interview with the Bureau, only to be caught out later on.

He had been facing up to five years in prison and was due to be sentenced the same day as the pardon.

The website Engadget says it is not clear why Cartwright is receiving the pardon.

He was the Vice Chairman of the Joint Chiefs of Staff from his nomination in 2007 through to his retirement from Marine Corps service in 2011, but was never Obama's favorite.

One suggestion is that the outgoing White House administration wants to put a lid on discussion of Stuxnet.

It's possible that the guilty plea and pardon could spare the government from disclosing secrets that may have shown the U.S. and Israel were behind a cyber attack on Iran's nuclear facilities, just a deal with Iran was being finalized.

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Sanger's reports confirmed suspicions that the US and Israel engineered the computer virus Stuxnet to set back Iran's nuclear program (pictured, Iranian president Mahmoud Ahmedinejad at the Natanz uranium enrichment facility in 2008)

Cartwright falsely told investigators that he did not provide or confirm classified information contained in a news article and, later, in a book by New York Times journalist David Sanger, according to charging documents unsealed by prosecutors.

Neither the book nor the classified subject is identified in court papers. But Sanger wrote in his 2012 book 'Confront and Conceal' about the classified operation to attack Iran's nuclear facilities.

In a written statement released to reporters after the hearing back in October, Cartwright stressed that he was not the initial source of the leak about Stuxnet but spoke to reporters about material they already knew.

George W Bush started the operation code-named Olympic Games, and Obama preserved and expanded the program, leading to Stuxnet's deployment before it escaped onto the internet

'It was wrong for me to mislead the FBI on November 2, 2012, and I accept full responsibility for this,' Cartwright said. He added that his only goal in talking to reporters was 'to protect American interests and lives.'

Cartwright's attorney, Gregory Craig, said in a statement that his client 'was engaged in a well-known and understood practice of attempting to save national secrets, not disclosing classified information.'

The plea agreement said that between January and June of 2012, Cartwright 'provided and confirmed classified information' to Sanger. Cartwright also confirmed classified information in February 2012 to Klaidman that was included in an article for Newsweek magazine, the agreement said.

Sanger's book and the classified subject were not identified in court papers.

But Sanger has written extensively about Stuxnet, with the New York Times naming Cartwright as the mastermind behind the virus.

The virus would cause the centrifuges to spin out of control in the plant (pictured) while providing false feedback so it would appear as if things were running normally

Cartwright, who was known for taking unconventional strategies, presented George W. Bush in 2006 with the idea of using a 'sophisticated cyberweapon' to reach the computer system controlling Iran's Natanz plant, according to the NYTimes.

According to the Times, Obama preserved the operation after Bush's departure and ordered the cyber attacks sped up.

In 2010, Stuxnet successfully disabled 1,000 centrifuges that the Iranians were using to enrich uranium.

The virus, initially delivered through a thumb drive inside the plant, would cause the centrifuges enriching nuclear fuel to spin out of control.

But what set Stuxnet apart from any other virus, was its ability to adapt.

The bug would remain undetected as it spied on the targeted system, and then provide false feedback when it attacked, so it would appear as if things were running normally.

Each attack was different, and the virus could also access the internet to download more recent versions of itself.

Former chief of the CIA Michael Hayden told the Times: 'Previous cyber attacks had effects limited to other computers. This is the first attack of a major nature in which a cyber attack was used to effect physical destruction [...] Somebody crossed the Rubicon.'

The Times said Cartwright was one of the crucial players who had to break the news to Obama and Vice President Joe Biden that Stuxnet at one point had escaped onto the Internet.

An element of the program accidentally became public in the summer of 2010 because of a programming error that allowed it to escape, the Times reported.

When that happened, top administration officials met to consider whether the program had been fatally compromised and Obama decided to proceed.

When reports about Stuxnet emerged, congressional leaders demanded a criminal investigation and Obama said he had zero tolerance for such leaks.